Contrary to what you say, recent versions of Ghostscript have become quite efficient when it comes to merging multiple PDFs into a single one, and at the same time avoiding to embed an identical font multiple times.
Inputs
Here are the details about 3 input PDFs, which I'll merge into a single output:
for i in {1..3}; do pdffonts ${i}.pdf ; echo ; done
name type encoding emb sub uni object ID
-------------------------- ----------------- ---------------- --- --- --- ---------
Helvetica Type 1C WinAnsi yes no no 8 0
name type encoding emb sub uni object ID
-------------------------- ----------------- ---------------- --- --- --- ---------
Helvetica Type 1C WinAnsi yes no no 8 0
name type encoding emb sub uni object ID
-------------------------- ----------------- ---------------- --- --- --- ---------
Helvetica Type 1C WinAnsi yes no no 8 0
Merging
Now merge these three PDF input files with the help of pdftk.
pdftk 1.pdf 2.pdf 3.pdf cat output merged.pdf
Output
Now check the font status of the output merged.pdf:
pdffonts merged.pdf
name type encoding emb sub uni object ID
-------------------------- ----------------- ---------------- --- --- --- ---------
Helvetica Type 1C WinAnsi yes no no 5 0
Helvetica Type 1C WinAnsi yes no no 14 0
Helvetica Type 1C WinAnsi yes no no 23 0
Ok, not yet there...
Optimize with Ghostscript
gs -o optim.pdf -sDEVICE=pdfwrite merged.pdf
GPL Ghostscript GIT PRERELEASE 9.27 (2018-11-20)
Copyright (C) 2018 Artifex Software, Inc. All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
Processing pages 1 through 3.
Page 1
Page 2
Page 3
Check font statuses and file sizes
ls -lh {1..3}.pdf merged.pdf optim.pdf
-rw-r--r-- 1 kurtpfeifle staff 51K Dec 31 20:25 1.pdf
-rw-r--r-- 1 kurtpfeifle staff 51K Dec 31 20:25 2.pdf
-rw-r--r-- 1 kurtpfeifle staff 51K Dec 31 20:25 3.pdf
-rw-r--r-- 1 kurtpfeifle staff 147K Dec 31 20:32 merged.pdf
-rw-r--r-- 1 kurtpfeifle staff 7.5K Dec 31 20:34 optim.pdf
Conclusion
I tested this with Ghostscript v9.25.
If this doesn't work for you, you'll need to...
- ...tell us the version of Ghostscript you are using;
- ...provide a link to (some of) your input PDFs for more detailed analysis.
I'm aware that this answer does not provide you with a solution that meets exactly your license requirements. -- But your false statement about Ghostscript prompted me to give this answer anyway, so other people interested in this topic can still benefit from it...